KZ550 LTD Vacuum routing

I have a 1983 KZ550 LTD that has sat about 8 years, without running. I bought it and rode it one summer. It never ran reliably before, and I'm working through it to get it going again. One thing i distinctly remember from eight years ago, was the bike wouldn't start if it was les than 60 degrees F out. So far this winter I have:

• Changed oil and filter 3L 10W-40
• Changed Spark plugs (NGK 2120 D8EA)
  • Verified good spark on all four by grounding against engine and firing the starter
• Change engine air filter element (Hi Flo)
• Installed new airbox boots (PNs 11015-063, 11015-057)
• Installed new engine intake boots (PN <!--td {border: 1px solid #cccccc;}br {mso-data-placement:same-cell;}-->16065-1014) and clamp rings
• Installed new mighty mag AGM battery
• removed and cleaned all four carburetors, verified choke valves and choke lever working properly
  • Removed float bowls, pilot and main jets, used small brushes, carb cleaner, compressed air and scrubbed them all out 

After I did all of the above, it was not even 45 deg F, but i went for it anyway. It did not start until I heated up the engine block with a space heater for a while. When its running, it backfires above 3k rpm everytime you pull throttle. The bike is equipped with an air switch valve, PN 16126-1017. There are four lines from it:

• Two large ones that go to either side of the motor
• One large one hat runs directly to the air box
• One smaller line, ~.250" DIA that splits into a tee and I'm not sure where this goes - see attached photo

So there is the pretext. My questions are around the two things I've noticed since I got it running:

1. Header/ exhaust #4 (If sat on the bike, left to right are 1,2,3,4) does not heat up like the other three. Only seems warm by proximity to the hot exhaust next to it. So, possible issue with carb or cylinder #4, or something else?
   1. I removed the top cap on carbs #3 and #4 (did not do this on the other two carbs) and cleaned inspected the inside, looked fine no major crud. 
   2. Removed 
2. I do not know what ports to plug and what to use as vacuum from the petcock?
   1. The bike had two open ports on the intake boots (between carb and engine) on carbs 1 and 4
   2. port #2 has a black line from it, but it was not terminated anywhere
   3. port three was capped
   4. This bike has a vacuum line from the petcock, where does this line terminate? 
   5. See first attached photo - one black line from a rail between carb 3 and 4, with an open port right next to it
      1. What to do with these?

TL:DR - I basically need to know:

• What ports/ nipples to close off, and which to use. Of the ones I need to use, where do they run to and from? 
• What would cause the 4th header/ exhaust to not warm up with the others? Gunky carb, misfire, bad spark plug?

Vacuum is vacuum and does not matter where it comes from, as long as is from engine intake.

In newer Kawi 4 aircooled engines, the vacuum nipples for the air injection valves come from carbs 1 & 4 nipples,....the vacuum for the petcock come from carbs 3 & 4, (one is enough), but like I said it does not matter which carb.

Whatever you do, don't run the engine with those nipples open to atmosphere.

I'm not too familiar with these carbs but I'm pretty sure that vacuum was supplied from the two outside carbs to the air switch valve on top of the engine, another line to the petcock, and the last one is capped off. A lot of people get rid of the air switch valve and cap off all the ports.

Regarding your issue, I would check the pilot circuit and make sure that everything goes through well. Make sure that the pilot jet is not corroded on the inside. Make sure that the float bowl level is at spec for each carb by either measuring the height of the float bowl or using the clear tube method and check that your fuel/air mixture screw is set at stock amount of turns out.  That usually fixes most problems. If it doesnt fix it bogging at 3k rpm, check the ignition advancer unit for free rotation under the cover on the right side of the engine.

Edit: I also forgot, make  sure your carbs are synced and there are no leaks around the carbs at the carb holders. Check by spraying starting fluid or carb cleaner of the sorts around the carb holders. If the rpms go up, you probably have a leak.